This vignette describes the
one-time infrastructure steps required to deploy
roreviewapi on a Digital Ocean droplet, including the
editor volunteer search feature introduced in v0.2. Endpoints for that
feature are described in the editor
search vignette.
The Software Peer Review Lead should set up a regular alert system to automatically check the deployment status. This bash script issues an alert if anything is wrong:
#!/usr/bin/env bash
URL="https://reviewbot.ropensci.org"
status=$(curl -s -o /dev/null -w "%{http_code}" "$URL")
if [[ "$status" != "404" ]]; then
echo -e "reviewbot is down"
exit 1
fiThat should then be regularly called, for example by calling it
within a ~/.bashrc file, or via a local cron job.
Secrets are not stored in the
Dockerfile or anywhere else in the git repository. They
live in a .env file that exists only on the droplet, is
listed in .gitignore and .dockerignore, and is
injected into the plumber container at runtime via
env_file: .env in docker-compose.yml. Because
the file is untracked, git pull never overwrites it, and
the values never end up in an image layer.
Create .env in the project directory on the droplet,
with one KEY=value entry per line (no quotes and no
export), and restrict its permissions:
| Variable | Description |
|---|---|
GITHUB_PAT |
GitHub personal access token (also used as
GITHUB_TOKEN) |
PKGCHECK_TOKEN |
pkgcheck authentication token |
GMAIL_SENDER |
Sender address used for outgoing emails |
GMAIL_OAUTH_CLIENT_SECRET |
Path to the Google OAuth client secret JSON file,
e.g. /data/email/<client_secret>.json |
GMAIL_TOKEN_CACHE |
Path to the cached Gmail token,
e.g. /data/email/gmailr_token |
GMAIL_AUTH_EMAIL |
Google account used to authenticate with Gmail |
AIRTABLE_API_KEY |
AirTable personal access token |
AIRTABLE_BASE_ID |
ID of the AirTable base containing the EiC rotation table |
ROREVIEWAPI_BASE_URL |
Public HTTPS base URL of the deployed API
(https://reviewbot.ropensci.org) |
At container start, docker-entrypoint.sh writes these
values to ~/.Renviron (setting GITHUB_TOKEN
from GITHUB_PAT, and ROREV_CONTAINER=true), so
that R can read them, and then starts the API. To change a secret, edit
.env on the droplet and re-run restart.sh; no
change to the Dockerfile is needed.
The two GMAIL_* file paths must be inside
/data/email/, which is the container side of the
bind-mounted data directory (see Droplet
preparation). Place the corresponding files in
/srv/roreviewapi/data/ on the droplet. That mount must
remain read-write, because the Gmail token cache is written back during
authentication.
data.records:read scope on the relevant base. Set this as
AIRTABLE_API_KEY.https://airtable.com/appXXXXXXXX/...). Set this as
AIRTABLE_BASE_ID.The editor-in-chief-rotation table within that base must
have period_start, period_end, and
acting_eic_email fields.
Create the persistent data directory that will be bind-mounted into the container. This directory holds the SQLite database, the notify-email cache file, and the Gmail OAuth client secret and token cache files, and must survive container rebuilds.
Ask your DNS administrator to add an A record pointing
your chosen subdomain to the droplet’s IP address, for example:
review.example.org. IN A <droplet-ip>Allow up to 24 hours for propagation, though it is usually much faster.
Once the DNS record is live, obtain a Let’s Encrypt certificate on
the droplet. The --standalone method requires port 80 to be
free (stop the running stack first if necessary):
The certificate and key are written to
/etc/letsencrypt/live/review.example.org/. Certbot installs
a systemd timer that renews certificates automatically; confirm it is
active:
The HTTP-01 challenge works by certbot binding a temporary server to port 80. Two things can prevent this:
Port 80 occupied. The Docker stack must be stopped before running certbot, otherwise nginx holds port 80 and the challenge fails immediately:
Port 80 blocked by a firewall. There are two independent firewalls to check:
Droplet firewall (ufw):
If ufw is active and port 80 is not listed, open it:
Digital Ocean cloud firewall: in the DO console under Networking → Firewalls, confirm there is an inbound rule allowing TCP port 80 from all sources. The cloud firewall sits in front of the droplet and blocks traffic before it reaches ufw, so both layers must allow port 80.
To confirm DNS has propagated before retrying certbot, check that the A record resolves to the droplet IP:
Set NGINX_SERVER_NAME in the environment before starting
the stack — this value is substituted into nginx.conf at
container startup. Ensure .env exists (see Environment variables), then:
Routine redeployment is handled by restart.sh, which
runs git pull --ff-only, tears down and rebuilds the stack,
and brings it back up. It is intended to be called from cron. It locates
the project directory from its own path, so it needs no editing, but
.env must sit alongside it. Since .env is
untracked, secrets persist across pulls.
The compose file:
/srv/roreviewapi/data into the plumber container
at /data/email, and sets
ROREVIEWAPI_EMAIL_DB=/data/email/searches.sqlite so the
SQLite database persists across rebuilds..env via env_file./etc/letsencrypt read-only into the nginx
container so the certificate is available.restart.sh is run on a schedule so that the droplet
picks up new commits and rebuilds fresh images without manual
intervention. One authorized admin of the Digital Ocean droplet needs to
configure the cron job.
The job must run as a user that can run docker-compose
(either root or a member of the docker group). The
following uses root’s crontab, so that the log file below can be written
to /var/log.
Check whether a job already exists (see “Viewing current jobs” below), to avoid creating a duplicate.
Open the crontab for editing; if prompted, choose an editor
(nano is the easiest):
Add the following line, replacing the path with the absolute path to the project checkout on the droplet:
This runs the script at 00:00 every Tuesday. The five leading fields are minute, hour, day of month, month, and day of week (0–7, where both 0 and 7 are Sunday). crontab.guru is useful for checking a schedule. The trailing redirect appends all output, including errors, to a log file.
Save and exit. Cron picks up the change automatically; no restart of the cron service is needed.
An absolute path is required because cron does not run in the project
directory. restart.sh finds the project directory (and thus
.env) from its own location, so it needs no other
configuration.
List the jobs in root’s crontab with:
Omit sudo to list the current user’s own crontab
instead. Each user has a separate crontab, so if nothing appears, check
the other user (or root) that may have been used to set the job up.
Re-open the crontab with sudo crontab -e, edit the line
(for example, change the schedule fields), and save. To disable the job
without deleting it, comment the line out by prefixing it with
#; to remove it, delete the line. Confirm the result with
sudo crontab -l.
Maintenance falls into two parts with very different transfer costs:
.env changes.When the new person only deploys and debugs, and the existing authorizing account stays active:
sudo access on the droplet.roreviewapi GitHub repository.ro-auto-email Google Cloud project’s
IAM..env
(securely, for example via a password manager rather than email or
chat).This is required if the outgoing maintainer’s accounts will become
unusable, for example on leaving the organization. The values in
.env that are tied to a person are:
| Variable | Tied to | Action on transfer |
|---|---|---|
GITHUB_PAT |
GitHub account that created it | Replace with a token created by the new maintainer |
AIRTABLE_API_KEY |
AirTable account that created it | Replace with a token created by the new maintainer (see AirTable for the required scope) |
GMAIL_AUTH_EMAIL, GMAIL_TOKEN_CACHE |
Google account that authorized gmailr |
Replace, following the Gmail transfer steps in the editor search vignette |
GMAIL_OAUTH_CLIENT_SECRET,
GMAIL_SENDER |
Google Cloud project and the reviewbot@ropensci.org
alias |
Unchanged if the same Cloud project and alias are kept |
AIRTABLE_BASE_ID, ROREVIEWAPI_BASE_URL,
PKGCHECK_TOKEN |
Not tied to a person | Unchanged unless the base, URL or pkgcheck service changes |
The steps are then:
The new maintainer creates their own GitHub and AirTable personal access tokens, and completes the Gmail steps in the editor search vignette.
Update .env on the droplet with the new
values.
Run restart.sh (or wait for the next scheduled run)
so that the container picks up the new .env and
credentials:
Verify that the editor search workflow still sends and receives emails (see the editor search vignette).
Once the new setup works, the outgoing maintainer should revoke their old GitHub and AirTable tokens, and the old Google grant.
git config lines in
the Dockerfile hold the user.name and
user.email used for commits made inside the container.